Increasing Stemness Drives Prostate Cancer Progression, Plasticity, Therapy Resistance and Poor Patient Survival

BackgroundCancer progression is often accompanied by dedifferentiation and acquisition of stem cell-like properties (stemness). In prostate cancer (PCa), lineage plasticity and therapy resistance remain major clinical challenges, yet a unified quantitative transcriptomic framework connecting stemness, androgen receptor (AR) signaling, castration resistance, and disease progression across the PCa continuum is lacking. MethodsWe performed an integrative analysis of 87,192 transcriptomic data from 27 preclinical and clinical datasets spanning the PCa continuum--from normal prostate and treatment-naive primary PCa (Pri-PCa) to PCa treated with neoadjuvant ADT (nADT) and metastatic castration-resistant PCa (mCRPC). Tumor stemness was quantified using a transcriptome-derived mRNAsi Stemness Index (Stemness for short), and a 12-gene PCa-Stem signature was developed to capture PCa-specific stemness. Canonical AR activity (c_AR-A) and castration-reprogrammed AR activity (cr_AR-A), RB1-loss, PTEN-loss, and MYC activity signature scores were analyzed across cohorts, with survival assessed in multiple datasets. Functional validations included MYC knockdown RNA-seq data analysis in LNCaP cells and siRNA-mediated depletion of representative PCa-Stem genes in androgen-independent LAPC4 (LAPC4-AI) cells. ResultsThe Stemness score and c_AR-A increased concordantly during early prostate tumorigenesis but diverged with PCa progression: as Gleason grade increased, c_AR-A declined while Stemness continually increased. mCRPC exhibited the highest Stemness and lowest c_AR-A, a pattern recapitulated in Pten/Rb1/Trp53-deficient mouse models. Both global Stemness score and the PCa-Stem signature were enriched in aggressive PAM50-LumB and PCS1 subtypes, associated with the proliferative and lineage plasticity programs, and predicted poor survival. Depletion of representative PCa-Stem genes (HMMR, PBK, AURKB) suppressed proliferation, invasion and organoid formation in LAPC4-AI cells. Mechanistically, MYC activity, cr_AR-A and RB1-loss transcriptomic signature were consistently associated with and drove pervasively increasing Stemness during PCa progression. Shared mitotic regulators linked cr_AR-A, RB1-loss, MYC activity, and PCa-Stem to mitotic control and therapy-resistant proliferation. ConclusionsThe Stemness scores reported herein quantitatively capture PCa aggressiveness, plasticity, treatment resistance and progression, and prognosticates poor patient survival. Therapy-reprogrammed AR activity (cr_AR-A), RB1 loss, and MYC activation together reinforce the high-Stemness state and therapy resistance in mCRPC. Collectively, our work establishes a trajectory-integrated and scalable transcriptomic framework that defines cancer Stemness as a quantifiable clinical determinant of PCa progression, plasticity, progression, therapy resistance and patient survival.